dgmacarthur | April 30, 2009This is a profoundly impressive paper - a study of the patterns of genetic variation in 2,400 individuals from 113 African populations, by far the most comprehensive analysis of African genetic diversity ever performed.
I had heard that Sarah Tishkoff's group had assembled a large
collection of African DNA samples, a daunting achievement in itself
given the logistical, ethical and social challenges involved (New Scientist
notes that "the researchers often had to use their vehicle batteries to
power the
centrifuges used to separate out white blood cells from their samples")
- but the breadth…
dgmacarthur | April 30, 2009For those who have been too distracted by swine flu to notice: shares of the biotech company Sequenom have plummeted by 77% after the company announced that the extremely promising initial results for its SEQureDx Down syndrome test - which is designed to detect Down syndrome fetuses using blood samples from pregnant women - were "questionable" and had been mishandled by employees.
GenomeWeb Daily News reports:
As of early February, Sequenom had released data on
its SEQureDx test from a total of 858 samples. It said that the
positive predictive value was 96.6 percent, and the negative…
dgmacarthur | April 28, 2009A new paper in Nature reports the results of a large genome-wide association of autism. After some fairly heroic data analysis, the researchers have managed to tag one region of the genome as containing a common variant that contribute to the disease, with odds ratios on the order of 1.2 (the paper actually reports six variants in the same region, but these all appear to be tagging the same underlying causal variant).
The finding is getting fairly glowing press coverage, but let's keep it in context: an odds ratio of 1.2 means that individuals carrying the variant have their risk of the…
dgmacarthur | April 28, 2009Cho, Y., Go, M., Kim, Y., Heo, J., Oh, J., Ban, H., Yoon, D., Lee, M., Kim, D., Park, M., Cha, S., Kim, J., Han, B., Min, H., Ahn, Y., Park, M., Han, H., Jang, H., Cho, E., Lee, J., Cho, N., Shin, C., Park, T., Park, J., Lee, J., Cardon, L., Clarke, G., McCarthy, M., Lee, J., Lee, J., Oh, B., & Kim, H. (2009). A large-scale genome-wide association study of Asian populations uncovers genetic factors influencing eight quantitative traits Nature Genetics, 41 (5), 527-534 DOI: 10.1038/ng.357
A paper just released in Nature Genetics takes the most comprehensive look yet at the genetic factors…
dgmacarthur | April 27, 2009This seems like pretty interesting news:
23andMe, Inc., an industry leader in personal genetics, and Palomar Pomerado Health
(PPH), the largest public health district in California, today
announced that PPH will be offering the 23andMe Personal Genome Service
for sale to San Diegans at its outpatient health centers. As an
innovator in preventive health care, PPH encourages its communities to
understand their genetic information in order to make more informed
decisions about their health. This partnership marks the first time
that a healthcare organization has provided the Personal Genome…
dgmacarthur | April 27, 2009I usually try to maintain a fairly single-minded focus on genomics on this blog, but Alex Wild's current series of post on insect photography over at Photo Synthesis is simply stunning. Anyone interested in either photography or entomology - or simply appreciative of a beautiful image - should wander over and check them out.
Alex's rotation on Photo Synthesis may soon be coming to an end, but you can then follow him back to his usual home, Myrmecos.
Here's a classic example of Alex's work:
Subscribe to Genetic Future.
dgmacarthur | April 26, 2009The Personal Genome Project, an initiative founded by George Church that ultimately seeks to sequence the complete genomes of 100,000 people, has called for the next wave of volunteers. The PGP will sequence your genome and give you back the data for the bargain-basement price of zero dollars (not bad compared to the $68,000 that the Knome auction is starting at).
The benefits to volunteers are straightforward: you get access to your own genome sequence before most human beings on the planet, and you get the warm fuzzy glow that comes with benefiting humanity. I'm not being at all sarcastic…
dgmacarthur | April 25, 2009The auction of a whole-genome sequencing service that I scoffed at a few days ago is now live on eBay - serious bidders only, please, and bids start at $68,000.
Here's what you get for your suitcase of cash:
Personal whole genome sequencing and comprehensive interpretation of your genome.
Knome's proprietary KnomeXplorer⢠genome browser software to navigate and explore your own genome.
Two years of Knome's update service allowing you to remain current on the latest cutting-edge genetics research.
A digital copy of your whole genome sequence on Knome's security encrypted GenomeKey [an…
dgmacarthur | April 24, 2009Associated Press reports that Germany will likely soon pass regressive laws limiting the use of genetic testing:
The German parliament approved legislation Friday limiting the use
of genetic testing in an effort to prevent the technology's abuse.
The law, which was debated for more than seven years, must still go
before the upper house of parliament, but it is not expected to meet
any resistance.
Under the law, genetic tests can only be carried out by a doctor
and require the full consent of all parties involved. That makes it
illegal to conduct anonymous paternity tests and anyone found in…
dgmacarthur | April 22, 2009Personal genome sequencing provider Knome is planning to offer a complete genome sequence to the highest bidder on eBay - with the bidding opening at $68,000.
The plan, announced in an NY Times article today, is described as "essentially a publicity stunt" - the proceeds will be donated to the X Prize Foundation, a charitable trust devoted to providing cash incentives for reaching technological breakthroughs. The breakthrough that Knome is most interested in seeing achieved, of course, is the goal of the Archon X Prize for Genomics: a reward of $10 million for the first group to sequence 100…
dgmacarthur | April 22, 2009Nutrigenomics is a word typically associated with shady companies trying to use genetic tests to sell you expensive diets - but GenomeWeb News reports that the area may finally be receiving some legitimate scientific attention:
The Salk Institute today said that it will use a $5.5 million grant
from the Leona M. and Harry B. Helmsley Charitable Trust to create a
center to study nutritional genomics.
The La Jolla, Calif.-based institute will use the funding to launch
the Salk Center for Nutritional Genomics, which will study the effects
of nutrition and genetic interactions on metabolism, the…
dgmacarthur | April 22, 2009I ranted yesterday about two misleading pieces in the Telegraph (an opinion piece from Steve Jones, and a follow-up article) that sequentially converted a debate between scientists over the value of genome-wide association studies and the future of genetic research into a broader indictment of the last few years of common disease genetics.
Mark Walport, director of the Wellcome Trust (a major funder of genomic research), has responded today in a letter to the Telegraph (a third of the way down the page). Here's the text of the letter:
Genetic research vital
SIR - Professor Steve Jones is…
dgmacarthur | April 21, 2009A paper just published online in Nature Genetics describes a brute force approach to finding the genes underlying serious diseases in cases where traditional methods fall flat. While somewhat successful, the study also illustrates the paradoxical challenge of working with large-scale sequencing data: there are often too many possible disease variants, and it can be extremely difficult to work out which are actually causing the disease in question.
The authors looked at 208 families where multiple members suffered from mental retardation and where the family history was consistent with the…
dgmacarthur | April 21, 2009I wrote a few days ago about a debate in the New England Journal of Medicine over the value of data emerging from recent genome-wide studies of the role of genetic variation in common human diseases and other traits. David Goldstein argued that genome-wide association studies (GWAS) have generated disappointing results, and should be scaled back in favour of whole-genome sequencing; Joel Hirschhorn responded with an upbeat piece emphasising the insights generated by GWAS into the molecular basis of common diseases.
Now geneticist Steve Jones has an opinion piece in the Telegraph that…
dgmacarthur | April 20, 2009Mark Henderson reports that an influential UK think-tank, the Nuffield Council on Bioethics, has launched an inquiry into personalised medicine:
The Nuffield working party includes nine scientists, social scientists,
lawyers and philosophers. It will consider whether genetic tests ought to be
regulated more tightly, and whether people who buy them and then consult
their GPs about the results should have to pay for such follow-up advice.
The inquiry will also examine other aspects of direct-to-consumer healthcare,
such as MRI and CT scans [...] Hugh
Whittall, director of the Nuffield Council,…
dgmacarthur | April 19, 2009Jonathan Eisen summarises the major themes from the Joint Genome Institute meeting. He has a numbered list of 20 highlights - here's a few that I thought would be of most interest to Genetic Future readers:
2. Ecological and population genomics are truly the next big thing. 3. Related to the above point, one of the next revolutions is going to be in high throughput phenotyping --- after all, we cannot solve the genotype-phenotype problem when we only know the genotype.Â
5. NextGen sequencing has completely outrun the ability of even good bioinformatics people to keep up with the data and…
dgmacarthur | April 19, 2009John Hawks riffs on the themes of a recent Economist article on personal genomics (which I've also talked about here).
Hawks argues that "nobody's quite figured out how to sell sequence to people" - that although 23andMe's marketing strategy is shrewd, it's still "marketing based on anxiety", and the provided content initially didn't seem that appealing:
I used to feel the way Altshuler does. What good could it possibly do to have my genes sequenced? I know the limits on the usefulness of the data. There's minimal medical value for most people right now. I'm not even sure what I would do…
dgmacarthur | April 16, 2009A reader pointed me to a recent Economist article on personal genomics. There are numerous tidbits of interest, such as a passing comment about the chaotic Chinese personal genomics industry (about which I know almost nothing). Perhaps the most important quote comes in the closing paragraph:
Dr Church even argues that genome sequencing "will in effect be available free" because companies will give away sequencing to sell other services, such as genetic interpretation--much as mobile operators "give away" handsets to get customers to sign up for lucrative service plans. And when this happens…
dgmacarthur | April 16, 2009Mary Mangan at Open Helix predicts that personal genomics will trigger the appearance of a brand new eating disorder: geneorexia nervosa.
...there will be a proportion of people who take their genetic information
(which I know is of varying utility at best right now to those who have been sequenced ), and they'll change
their diets. They'll upend their and their family's lifestyles. They will be
in fear of substances, of foods, of fabrics, of everything-beyond reason. And
they'll buy products and services of dubious quality-even potentially dangerous
ones.
I do agree that widespread…
dgmacarthur | April 16, 2009The latest issue of the New England Journal of Medicine has four excellent and thought-provoking articles on the recent revolution in the genetics of common disease and its implications for personalised medicine and personal genomics. Razib and Misha Angrist have already commented, and there's also a thorough lay summary by Nick Wade in the NY Times.
The scene is set by a brief but useful review of progress in genome-wide studies of human disease, which is worth reading if you need to get yourself up to speed on the scope of progress in modern disease genomics. The main course, however, is…